threads: Error calling pthread_setaffinity_np: 22

[Hermes Escalona]

Hi Alex,

I have a large dataset and got from the parse option that I need 315 threads, but when running raxmlNG with more than 10 threads got this error: Error calling pthread_setaffinity_np: 22

Any hints? maybe an installation issue?

best,

HE

[Alexey Kozlov]

Hi Hermes,

do you have >10 CPU cores in your system? How exactly do you call
raxml-ng (command line and/or submission script)?

Best,
Alexey

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[Hermes Escalona]

Hi Alex,

YES, more than 10 CPU cores.

here is the sbatch:

#SBATCH --time=90:00:00

#SBATCH --mem=200GB

#SBATCH --nodes=1

#SBATCH --ntasks-per-node=1

#SBATCH --cpus-per-task=20

#SBATCH --job-name=raxml_NG

module load gcc/8.1.0

module load mpich/3.3.0

/data/esc003/apps/raxml-ng/bin/raxml-ng-mpi --msa alignments.fasta --model partition.nex --seed 2 --threads 20

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--

Hermes E. Escalona

mob. +61 0432142826

https://hermesescalonaweb.wordpress.com

[Alexey Kozlov]

hm, that's weird, you can disable thread pinning by adding

--extra thread-nopin

but please double-check thread pinning manually if possible (e.g. with
htop)

Best,
Alexey

On 20.02.19 23:51, Hermes Escalona wrote:
> Hi Alex,
>

> YES, more than 10 CPU cores.
>
> here is the sbatch:
>
> #SBATCH --time=90:00:00
> #SBATCH --mem=200GB
> #SBATCH --nodes=1
> #SBATCH --ntasks-per-node=1
> #SBATCH --cpus-per-task=20
> #SBATCH --job-name=raxml_NG
>
> module load gcc/8.1.0
>
> module load mpich/3.3.0
>
> /data/esc003/apps/raxml-ng/bin/raxml-ng-mpi --msa alignments.fasta
> --model partition.nex --seed 2 --threads 20
>
>
>
> .El jue., 21 feb. 2019 a las 9:19, Alexey Kozlov

> (<alexei...@gmail.com <mailto:alexei...@gmail.com>>) escribió:

>
> Hi Hermes,
>
> do you have >10 CPU cores in your system? How exactly do you call
> raxml-ng (command line and/or submission script)?
>
> Best,
> Alexey
>
> On 20.02.19 23:09, Hermes Escalona wrote:
> > Hi Alex,
> >
> > I have a large dataset and got from the parse option that I need 315
> > threads, but when running raxmlNG with more than 10 threads got this
> > error: Error calling pthread_setaffinity_np: 22
> >
> > Any hints? maybe an installation issue?
> >
> > best,
> >
> > HE
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.

> > For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.com>.

> For more options, visit https://groups.google.com/d/optout.
>
>
>
> --

> Hermes E. Escalona
>
> mob. +61 0432142826
> https://hermesescalonaweb.wordpress.com
>

[Hermes Escalona]

thanks Alex, --extra thread-nopin worked out!

I was suspecting that it may have something to do with the installation since I did it by myself.

cheers,

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